Nick Boyd
@nboyd.bsky.social
📤 87
📥 162
📝 24
oh, this is nice:
x.com/proteinbase/...
. only a few lines of code…
9 days ago
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Vote for
@martinpacesa.bsky.social
‘s designs in the adaptyv nipah virus competition:
proteinbase.com/collections/...
. because they’ll actually bind
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Submission 1
This is a submission to the Nipah Binder Competition competition.
https://proteinbase.com/collections/nipah-binder-competition-submission-1-y562XeT6-H
10 days ago
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always amazes me that you can take code written on an A10, change a single line and get power utilization like this in JAX
28 days ago
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hack to get more diverse binders out of BoltzGen: sample an unconditional monomer, then sample a binder with secondary structure conditioning to match the monomer. this solves the long-standing open problem of generating 76 AA binders that aren't ubiquitin.
about 1 month ago
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Playing around with a JAX translation of
@gcorso.bsky.social
et al's BoltzGen (
github.com/escalante-bi...
). Super fun model! Has anyone tried skipping the inverse folding step for binder design? I'm wondering how well the all-atom designs do on their own...
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GitHub - escalante-bio/joltzgen: JAX translation of BoltzGen
JAX translation of BoltzGen. Contribute to escalante-bio/joltzgen development by creating an account on GitHub.
https://github.com/escalante-bio/joltzgen
about 1 month ago
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This paper is incredible; IMO large-scale, unbiased data is our best chance to get beyond the relatively small set of sequences that AlphaFold loves
add a skeleton here at some point
about 2 months ago
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proteinbase.com
from
@adaptyv.bio
looks amazing - hundreds of open-source binding affinity measurements. It’s hard to overstate the value of high-quality, uniform affinity data for training and evaluating filtering and ranking methods
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Proteinbase
The home of protein design data
https://proteinbase.com
2 months ago
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Another great post on binder design from
@btnaughton.bsky.social
!
add a skeleton here at some point
3 months ago
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Great nanobody design paper from
@brianhie.bsky.social
and
@synbiogaolab.bsky.social
! Amazing what combining a few public models can do
add a skeleton here at some point
3 months ago
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reposted by
Nick Boyd
3 months ago
Today we're dropping the "beta" tag from Adaptyv, launching our new website and announcing our $8M seed round. When we started Adaptyv a few years ago, our core belief was: AI models for biology are only as good as the lab data they're trained on and the hypotheses they can test in the real world.
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reposted by
Nick Boyd
Oli Clarke
3 months ago
Looks interesting (particularly for in silico affinity maturation) & code available on github:
github.com/TencentAI4S/...
add a skeleton here at some point
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Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here:
blog.escalante.bio/minibinder-d...
3 months ago
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reposted by
Nick Boyd
Boston Protein Design and Modeling Club
4 months ago
Have no fear if you weren't in the packed audience this week for
@martinpacesa.bsky.social
's awesome seminar, because you can check out the recording 👇
youtu.be/qQihl6If9vU
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BindCraft: one-shot design of functional protein binders
YouTube video by Boston Protein Design and Modeling Club
https://youtu.be/qQihl6If9vU
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reposted by
Nick Boyd
Patrick Kidger
6 months ago
✨Cradle is hiring protein+ML researchers!✨ We operate ML for lab-in-the-loop lead optimization across all industries (pharma, synbio, ...), modalities (antibodies, enzymes, ...), properties (binding, activity, ...) We're a scaleup and already relied upon by 4 of the top 20 big pharma. Apply here!
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Machine Learning Researcher in Protein Design (f/m/*)
Join a scaleup researching and operating ML-guided lead optimization of proteins. This means developing a combination of protein language models, and multi-property prediction and generation.
https://jobs.ashbyhq.com/cradlebio/92f8b4ed-2ab3-4619-9687-c5bbc9b1b543
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We added Boltz-2 to our protein design package! Under the hood this relies on a JAX translation, which, thanks to
@jeremywohlwend.bsky.social
and
@gcorso.bsky.social
’s clean code, was fairly easy to write. We’ve been getting great results -- and we have yet to explore the most exciting new features
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6 months ago
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Designed my (the?) first minibinder using
@gcorso.bsky.social
's new Boltz-2 model. Excited to explore how templates and increased MSA dropout impact binder design. This is work in progress but will be open sourced as usual
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6 months ago
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Want to try ESMC but don't want to switch from
#JAX
to pytorch? Here’s a super barebones translation to
@patrickkidger.bsky.social
's excellent equinox:
github.com/escalante-bi...
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GitHub - escalante-bio/esmj: jax translation of esmc
jax translation of esmc. Contribute to escalante-bio/esmj development by creating an account on GitHub.
https://github.com/escalante-bio/esmj
7 months ago
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